Resources Contact Us Home Browse by: INVENTOR PATENT HOLDER PATENT NUMBER DATE     Detection method using dissociated rolling circle amplification 7553619 Detection method using dissociated rolling circle amplification Patent Drawings: Inventor: Kumar, et al. Date Issued: June 30, 2009 Application: 10/072,666 Filed: February 8, 2002 Inventors: Kumar; Gyanendra (Guilford, CT) Abarzua; Patricio (West Caldwell, NJ) Egholm; Michael (Woodbridge, CT) Assignee: Qiagen GmbH (Hilden, DE) Primary Examiner: Chunduru; Suryaprabha Assistant Examiner: Attorney Or Agent: Ballard Spahr Andrews & Ingersoll, LLP U.S. Class: 435/6; 435/91.2; 536/24.33 Field Of Search: 435/6; 435/91.1; 435/91.2; 435/91.21; 536/23.1; 536/24.31; 536/24.33; 536/24.34; 536/24.32 International Class: C12Q 1/68; C07H 21/04 U.S Patent Documents: Foreign Patent Documents: 649066; 714486; 0 070 685; 0 128 332; 0 356 021; 0 379 369; 0 439 182; 0 466 520; 0 505 012; 0 667 393; 0 678 582; 0 745 690; 0 756 009; 2332516; 4262799; 4304900; 5146299; WO 91/08307; WO 92/01813; WO 94/16108; WO 94/24312; WO 95/03430; WO 95/03432; WO 95/22623; WO 95/25180; WO 95/35390; WO 96/33207; WO 97/17076; WO 97/17471; WO 97/19193; WO 97/20948; WO 97/42346; WO 98/04746; WO 99/18241; WO 99/31276; WO 00/04193; WO 00/15779; WO 00/36141; WO 00/71562; WO 01/40516; WO 01/61037; WO 01/64952; WO 01/77390; WO 01/79420; WO 01/88190; WO 01/97616; WO 02/00934; WO 02/02792; WO 02/053780; WO 02/077256; WO 02/103058; WO 03/008538; WO 2004/061119 Other References: Baner et al. Signal amplification of padlock probes by rolling circle replication. Nucleic Acids Res., vol. 26 (22), p. 5073-5078, 1998. citedby examiner. AAAI Board of Directors. Measurement of specific and nonspecific IgG.sub.4 levels as diagnostic and prognostic tests for clinical allergy. J. Allergy Clin. Immunol. 95:652-654 (1995). cited by other. Aliotta et al. Thermostable Bst DNA polymerase I lacks a 3'.fwdarw. 5' proofreading exonuclease activity. Genet. Anal (Netherlands) 12:185-195 (1996). cited by other. Anderson and Seilhamer. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18:533-537. cited by other. Beaucage et al. Deoxynucleoside Phosphoramidites-A New Class of Key Intermediates For Deoxypolynucleotide Synthesis. Tetrahedron Lett. 22:1850 (1981). cited by other. Boehmer and Lehman. Herpes Simplex Virus Type 1 ICP8: Helix-Destabilizing Properties. J. Virol. 67(2)711-715 (1993). cited by other. Brush. Dye Hard: Protein Gel Staining Products. The Scientist 12:16-22 (1998). cited by other. Chang. The pharmacological basis of anti-IgE therapy. Nat. Biotech. 18:157-162 (2000). cited by other. Chatterjee et al. Cloning and overexpression of the gene encoding bacteriophage T5 DNA polymerase. Gene 97:13-19 (1991). cited by other. Ekins. Ligand assays: from electrophoresis to miniaturized microarrays. Clin. Chem. 44(9):4015-2030 (1998). cited by other. Englisch et al. Chemically Modified Olinucleotides as probes and Inhibitors. Angewandte Chemie, International Edition 30(6):613-722 (1991). cited by other. Ernst et al. Cyanine Dye Labeling Reagents for Sulfhydryl Groups. Cytometry 10:3-10 (1989). cited by other. Fields et al. How many genes in the human genome. Nat. Genet. 7:345-346 (1994). cited by other. Fire and Xu. Rolling replication of short DNA circles. Proc. Natl. Acad. Sci. USA 92:4641-4645 (1995). cited by other. Fleischmann et al. Whole-Genome Random Sequencing and Assembly of Haemophilus influenzae Rd. Science 269:469 (1995). cited by other. Guo et al. Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotides arrays on glass support. Nucl. Acids Res. 22(24):5456-5465 (1994). cited by other. Gygi et al. Correlation between Protein and mRNA Abunance in Yeast. Mol. Cell. Biol. 19(3):1720-1730 (1999). cited by other. Hall et al., Nucleotide. Part XLI. Mixed Anhydrides an Intermediates in the Synthesis of Dinucleotide Phosphates. J. Chem. Soc. 3291-3296 (1957). cited by other. Hendrickson et al. High sensitivity multianalyte immunoassay using covalent DNA-labeled antibodies and polymerase chain reaction. Nucl. Acids Res. 23(3):522-529 (1995). cited by other. Henegariu et al. Custom flouscent-nucleotide synthesis as an alternative method foe nucleic acid labeling. Nat. Biotech. 18:345-348 (2000). cited by other. Hoy and Schimke. Bromodeoxyuridine/DNA analysis of replication in CHO cells after exposure to UV light. Mutation Res. 290:217-230 (1993). cited by other. Humphrey-Smith and Blackstock. Proteome Analysis: Genomics via the Output Rather Than the Input Code. J. Protein. Chem. 16(5):537-544 (1997). cited by other. Itakura et al. Synthesis and Using of Synthetic Oligonucleotides. Ann. Rev. Biochem. 53:323-356 (1984). cited by other. Iyer et al. 3-H-1,2-Benzodithiole-3-one 1, 1-Dioxide as an Improved Sulfuring Reagent in the Soild-Phase Synthesis of Oligodeoyribonucleoside Phosphorothioates. J. Am. Chem Soc. 112:1253-1254 (1990). cited by other. Jacobsen et al. The N-Terminal Amino-Acid Sequences of DNA Polymerase I from Escherichia coli and of the large and the Small Fragments Obtained by a Llimited Proteolysis. Eur. J. Biochem. 45:623-627 (1974). cited by other. Johnstone and Thorpe. Immunochemistry In Practice (Blackwell Scientific Publications) Oxford, England pp. 209-216 and 241-242 (1987). cited by other. Jung et al. Bacteriophage PRD1 DNA Polymerase: Evolution of DNA polymerases. Proc. Natl. Acad. Sci. USA 84:8287 (1987). cited by other. Kaboord and Bankovic. Accesory proteins function as matchmakers in the assembly of the T4 DNA polymerase holoenzyme. Curr. Biol. 5(2):149-157 (1995). cited by other. Kerkhof. A comparison of Substrates for Quantifying the Signal from a Nonradiolabeled DNA Probe. Anal. Biochem. 205:359-364 (1992). cited by other. Khrapko et al. Hybridization of DNA with Oligonucleotides Immobilized in Gel: A Convenient Method for detecting Single Base Substitutions. Mol. Biol. (Mosk) (USSR) 25:718-730 (1991). cited by other. Kong et al. Characterization of a DNA Polymerase from the Hyperthermophile Archaea Thermococcus litoralis. J. Biol. Chem. 268(3):1965-1975 (1993). cited by other. Langer et al. Enzymatic synthesis of biotin-labeled polynucleotides: Novel nucleic acid affinity probes. Proc. Natl. Acad. Sci. USA 78(11):6633-6637 (1981). cited by other. Lesnick and Freier. Relative Thermodynamic Stability of DNA, RNA, and DNA:RNA Hybrid Duplexes: Relationship with Base Composition and Structure. Biochemistry 34:10807-10815 (1995). cited by other. Letsinger et al. Use of a Stilbenedicarboxamide Bridge in Stabilizing, Monitoring, and Photochemically Altering Folded Conformations of Oligonucleotides. J. Am. Chem. Soc. 9:3655 (1976). cited by other. Lizardi et al. Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat. Genet. 19:225-232 (1998). cited by other. Matsumoto et al. Primary structure of bacteriophage M2 DNA polymerasee: conseved segments within protein briming DNA polymerases and DNA polymerase I of Escherichia coli, Gene 84:247 (1989). cited by other. Matteucci et al. Synthesis of Deoxyoligonucleotides on a Polymer Support. J. Am. Chem. Soc. 103:3185 (1981). cited by other. McGraw et al. Sequence-Dependent Oligonucleotide-Target Duplex Stabilities: Rules from Empirical Studies with a Set of Twenty-Mers. Biotechniques 8(6):674-678 (1990). cited by other. Mujumdar et al. Cyanine Dye Labeling Reagents Containing Isothiocyanate Groups. Cytometry 10:11-19 (1989). cited by other. Narang et al. Chemical Synthesis of Deoxyoligonucleaotides by the Modified Triester Method. Meth. Enzymol. 65:610-620 (1980). cited by other. Neilsen et al. Peptide Nucleic Acid (PNA). A DNA Mimic with a Peptide Backbone. Bioconjug. Chem. 5:3-7 (1994). cited by other. Neilsen. Sequence-Selective Recognition of DNA by Strand Displacement with a Thymine-Substituted Polymide. Science 254:1497-1500 (1991). cited by other. Oda et al. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. USA 96:6591-6596 (1999). cited by other. Patton et al. Components of the Protein Synthesis and Folding Machinery Are Induced in Vascular Smooth Muscle Cells by Hypertrophic and Hyperplastic Agents. J. Biol. Chem. 270(36):21404-21410 (1995). cited by other. Patton. Proteome analysis II. Protein subcellular redistribution: linking physiology to genomics via the proteome and separationtechnologies involved. J. Chromatogr. 722:203-223 (1999). cited by other. Patton. Making Blind Robots See: The Synergy Between Flourescent Dyes and Imaging Devices in Automated Proteomics. Biotechniques 28:944-957 (2000). cited by other. Pease et al. Light-generate oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl. Acad. Sci. USA 91(11):5022-5026 (1994). cited by other. Pless et al. Solid support synthesis of oligothymidylates using phosphorochlorides and 1-alkylimidazoles. Nucl. Acids Res. 2(6):773-786 (1975). cited by other. Rigler and Ramano. Differences in the Mechanism of Mechanism of Stimulation of T7 DNA Polymease by Two Binding Modes of Eschericha coli Single-stranded DNA-binding Protein. J. Biol. Chem. 270(15):8910-8919 (1995). cited by other. Rychlik et al. Optimization of the annealing temperature for DNA amplification in vivo. Nucl. Acids Res. 18(21):6409-6412 (1990). cited by other. Sambrook et al. Molecular Cloning: A Laboratory Manual, 2nd Ed. (Cold Spring Harbor Laboratory Press. Cold spring Harbor, N.Y.) Chapter 5-6 (1989). cited by other. Sanghvi. Heterocyclic Base Modifications in Nucleic Acids and Their Applications in Antisense Oligonucleotides. Antisense Research and Applications. (Crooke and Lebleu ed CRC Press) Chap. 15-16 pp. 273-301 (1993). cited by other. Sano et al. Detection of heavy methylation in human repetitive DNA subsets by a monoclonal antibody against 5- methylcytosine. Biochim. Biophys. Acta. 951:157-165 (1988). cited by other. Schena and Davis, Genes, genomes, and chipe. DNA Microarrays: A Practical Approach. Oxford University Press, New York pp. 1-16 (1999). cited by other. Siegel et al. A Novel DNA Helicase from Calf Thymus. J. Biol. Chem. 267(19):13629-13635 (1992). cited by other. Skaliter and Lehman. Rolling circle DNA replication in vitro by a complex of herpes simplex virus type 1-encoded enzymes. Proc. Natl. Sci. USA 91(22):10665-10669 (1994). cited by other. Speicher et al. Karyotying human chromosomes by combinatorial multi-flour FISH. Nature Genet. 12:368-375 (1996). cited by other. Stimpson et al. Real-time detection of DNA hybridization and melting on oligonucleotide arrays by using optical wave guides. Proc. Natl. Acad. Sci. USA 92:6379-6383 (1995). cited by other. Tsurumi et al. Functional Interaction between Epstein-Barr Virus DNA Polymerase Catalytic Subunit and Its Accessory Subunit in Vitro. J. Virol. 67(12)7648-7653 (1993). cited by other. Tyagi and Kramer. Molecular Beacons: Probes that Flouresce upon Hybridization. Nat. Biotech. 14:303-308 (1996). cited by other. Villemain and Giedroc. The N-Terminal B-Domain of T4 Gene 32 Protein Modulates the Lifetime of Cooperatively Bound Gp32-ss Nucleic Acid Complexes. Biochemistry 35:14395-14404 (1996). cited by other. Waggoner. Covalent Labeling of Proteins and Nucleic Acids with Fluorophores. Meth. Enzymol. 246:362-373 (1995). cited by other. Walker and Lin. Detection of Mycobacterium tuberculosis DNA with thermophilic strand displacement amplication and Fluorescence polarization. Clin. Chem. 42(10):1604-1608 (1996). cited by other. Wang et al. Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome. Science 280:1077 (1998). cited by other. Wansick et al. Fluorescent Labeling of Nascent RNA Reveals Transcription by RNA Polymerase II in Domains Scattered Throughout the Nucleus. J. Cell. Biol. 122(2):283-293 (1993). cited by other. Wirth and Romano. Stainig methods in gel electrophoresis, including the use of multiple detection methods. J. Chromatogr 698:123-143 (1995). cited by other. Yu et al. Cyanine dye dUTP analogs for enzymatic labeling of DNA probes. Nucl. Acids Res. 22(15):3226-3232 (1994). cited by other. Zhu and Ito. Purification and characterization of PRD1 DNA polymerase. Biochim. Biophys. Acta. 1219:267-276 (1994). cited by other. Zijderveld and van der Vliet. Helix-Destabilizing Properties of the Adenovirus DNA-Binding Protein. J. Virol. 68(2):1158-1164 (1994). cited by other. Loakes et al. "5-Nitroidole as a universal base analogue" Nucleic Acids Res. 1994, 22(20):45039-4043. cited by other. Baner et al. Signal Amplification of Padlock Probes by Rolling Circle Replication Nucleic Acids Research, Oxford University Press, Surrey, GB 26(22):5073-5078 (1998), XP002112357. cited by other. Gusev et al., Rolling Circle Amplfiication: A New Approach to Increase Sensitivity for Immunohistochemistry and Flow Cytometry American Journal of Pathology 159(1): 63-69 (Jul. 2001). cited by other. Mullenix et al. Allergen-specific IgE Detection on Microarrays Using Rolling Circle Amplification: Correlation with in Vitro Assays for Serum IGE Clinical Chemistry 47(10):1926-1929 (2001). cited by other. Nuovo et al. In Situ Amplification Using Universal Energy Transfer-Labeled Primers Journal of Histochemistry and Cytochemistry, Histochemical Society, New York, New York 43(3):273-279 (1999), XP008002684. cited by other. Schweitzer et al. Multiplexed Protein Profiling on Microarrays by Rolling-Circle Amplification Nature Biotechnology 20:359-365 (2002). cited by other. Schweitzer et al. Immunoassays with Rolling Circle DNA Amplification: A Versatile Platform for Ultrasensitive Antigen Detection PNAS 97(18):10113-10119 (2000). cited by other. Tyagia et al. Molecular Beacons: Probes that Fluoresce upon Hybridization, Nature Biotechnology, 14:303-308 (Mar. 1996), XP000196024. cited by other. Alves et al. Dot blot detection of point mutations with adjacently hybridising synthetic oligonucleotide probes. Nucleic Acids Res. 16(17):8723 (1988). cited by other. Arnold et al. Assay formats involving acridinium-ester-labeled DNA probes. Clin Chem. 35(8):1588-1594 (1989). cited by other. Ausubel et al. Current Protocols in Molecular Biology. John Wiley & Sons. 1:1.6.1-1.6.6 (1988). cited by other. Barany. Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc Natl Acad Sci USA. 88:189-193 (1991). cited by other. Barbato et al. Solid Phase Syntheses of Cyclic Oligodeoxyribonucleotides. Tetrahedron Letters. 28(46):5727-2728 (1987). cited by other. Bertina et al. Mutation in blood coagulation factor V associated with resistance to activated protein C. Nature. 369:64-67 (1994). cited by other. Birkenmeyer et al. DNA probe amplification methods. Journal of Virological Methods. 35:117-126 (1991). cited by other. Blanco et al. Characterization and purification of a phage .PHI.29-encoded DNA polymerase required for the initiation of replication. Proc Natl Acad Sci USA. 81:5325-5329 (1984). cited by other. Blanco et al. Highly efficient DNA synthesis by the phage .PHI.29 DNA polymerase. Journal of Biological Chemistry. 264(15):8935-8940 (1989). cited by other. Blanco et al. Terminal protein-primed DNA amplification. Proc Natl Acad Sci USA. 91:12198-12202 (1994). cited by other. Bonnet et al. Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc Natl Acad Sci USA. 96(11):6171-6176 (1999). cited by other. Broude et al. Enhanced DNA sequencing by hybridization. Proc Natl Acad Sci USA. 91:3072-3076 (1994). cited by other. Bryant et al. Phosphorothioate substrates for T4 RNA ligase. Biochemistry. 21(23):5877-5885 (1982). cited by other. Burgess et al. A new photolabile protecting group for nucleotides. Abstracts of Papers, Part 2.; 211.sup.th ACS National Meeting, American Chemical Society. New Orleans, LA, Mar. 24-28, 1996. cited by other. Butler et al. Bacteriophage SP6-specific RNA polymerase. Journal of Biological Chemistry. 257(10):5772-5778 (1982). cited by other. Capobianco et al. One pot solution synthesis of cyclic oligodeoxyribonucleotides. Nucleic Acids Research. 18(9):2661-2669 (1990). cited by other. Chetverina et al. Cloning of RNA molecules in vitro. Nucleic Acids Research. 21(10):2349-2353 (1993). cited by other. Christian et al. Detection of DNA point mutations and mRNA expression levels by rolling circle amplification in individual cells. Proc Natl Acad Sci U S A. 98(25):14238-14243. Epub Nov. 27, 2001 (Dec. 4, 2001). cited by other. Colantuoni et al., Gene expression profiling in postmortem Rett Syndrome brain: differential gene expression and patient classification. Neurobiol. Dis. 8(5):847-865 (2001). cited by other. Colantuoni et al., High throughout analysis of gene expression in the human brain. J. Neurosci. Res. 59(1):1-10 (2000). cited by other. Craxton et al. Linear Amplicifcation Sequencing, a Powerful Method for Sequencing DNA. Meth. Compan. Meth. Enzymol. 3(1):20-26 (Aug. 1991). cited by other. Crooke et al. Pharmacokinetic properties of several novel oligonucleotides analogs in mice. J Pharmacol Exp Ther. 277(2):923-937 (1996). cited by other. Cummins et al. Biochemical and physicochemical properties of phosphorodithioate DNA. Biochemistry. 35(26):8734-8741 (1996). cited by other. Daubendiek et al. Generation of catalytic RNAs by rolling transcription of synthetic DNA nanocircles. Nature Biotechnology. 15(3):273-277 (1997). cited by other. Daubendiek et al. Rolling-circle RNA synthesis: circular oligonucleotides as efficient substrates for T7 RNA polymerase. J Am Chem Soc. 117:7818-7819 (1995). cited by other. Davanloo et al. Cloning and expression of the gene for bacteriophage T7 RNA polymerase. Proc Natl Acad Sci USA. 81:2035-2039 (1984). cited by other. de Vroom et al. Syntheses of cyclic oligonucleotides by a modified phosphotriester approach. Nucleic Acids Research. 16(10):4607-4620 (1988). cited by other. Dean et al. Rapid Amplification of Plasmid and Phage DNA Using Phi29 DNA Polymerase and Multiply-Primed Rolling Circle Amplification. Genome Res. 11:1095-1099 (2001). cited by other. Diegelman et al. Generation of circular RNAs and trans-cleaving catalytic RNAs by rolling transcription of circular DNA oligoncleotides encoding hairpin ribozymes. Nucleic Acids Res. 26(13):3235-3241 (1998). cited by other. Doherty et al. Structural and mechanistic conservation in DNA ligases. Survey and Summary. Nucleic Acids Res. 28(21):4051-4058 (2000). cited by other. Dolinnaya et al. Oligonucleotide circularization by template-directed chemical ligation. Nucleic Acids Res. 21(23):5403-5407 (1993). cited by other. Dynal Technical Handbook. 2.sup.nd. Edition. Biomagnetic Techniques in Molecular Biology. 1. Solid-phase DNA sequencing. 9-34. (Dynal A.S., 1995). cited by other. Eckstein et al. Phosphorothioates in molecular biology. Trends in Bioch Sci. 14:97-100 (1989). cited by other. Erie et al. Melting Behavior of a Covalently Closed, Single-Stranded, Circular DNA. Biochemistry. 28:268-273 (1989). cited by other. Faruqi et al. High-throughput genotyping of single nucleotide polymorphisms with rolling circle amplification. BMC Genomics 2(4) (2001). cited by other. Gait. Oligonucleotides. Antisense Research and Applications. (Crooke et al, ed., CRC Press) Chapter 16; pp. 289-301 (1993). cited by other. Gasparro et al. Site-specific targeting of psoralen photoadducts with a triple helix-forming oligonucleotide: characterization of psoralen monoadduct and crosslink formation. Nucleic Acids Research. 22(14):2845-2852 (1994). cited by other. Gerdes et al. Dynamic changes in the higher-level chromatin organization of specific sequences revealed by in situ hybridization in nuclear halos. J Cell Biol. 126(2):289-304 (1994). cited by other. Gryaznov et al. Template controlled coupling and recombination of oligonucleotide blocks containing thiophosphoryl groups. Nucleic Acids Res. 21(6):1403-1408 (1993). cited by other. Guatelli et al. Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction molded after retroviral replication. Proc. Natl. Acad. Sci. USA 87:1874-1878 (1990). cited by other. Gunji et al. Correlation between the serum level of hepatitis C virus RNA and disease activities in acute and chronic hepatitis C. Int J Cancer. 52(5):726-730 (1992). cited by other. Guo et al. Enhanced discrimination of single nucleotide polymorphisms by artificial mismatch hybridization. Nature Biotechnology. 15:331-335 (1997). cited by other. Gupta et al. Expression of HIV-1 RNA in plasma correlates with the development of AIDS: a multicenter AIDS cohort study (MACS). Ninth International Conference on AIDS/Fourth STD World Congress. Jun. 6-11, 1993, Berlin, Germany. cited by other. Hacia et al. Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-color fluorescence anaylsis. Nature Genetics. 14:441-447 (1996). cited by other. Haff et al. Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry. Genome Res. 7(4):378-388 (1997). cited by other. Hagiwara et al. Quantitation of hepatitis C virus RNA in serum of asymptomatic blood donors and patients with type C chronic liver disease. Hepatology. 17(4)545-550 (1993). cited by other. Hall et al. Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction. Proc. Natl. Acad. Sci. USA 97. (15):8272-8277 (Jul. 2000). cited by other. Hanvey et al. Antisense and antigene properties of peptide nucleic acids. Science. 258:1481-1485 (1992). cited by other. Hata et al. Structure of the human omithine transcarbamylase gene. J Biochem. 103:302-308 (1988). cited by other. Heinonen et al. Simple triple-label detection of seven cystic fibrosis mutations by time-resolved fluorometry. Clin Chem. 43(7):1142-1150 (1997). cited by other. Hermanson et al., ed. Immobilized Affinity Ligands. (Academic Press, NY, 1992). cited by other. Hoeltke et al. Multiple nucleic acid labeling and rainbow detection. Anal. Biochem. 207:24-31 (1992). cited by other. Holland et al., Detection of Specific Polymerase Chain Reaction Product by Utilizing the 5' .fwdarw.3' Exonuclease Activity of Thermus aquaticus DNA Polymerase. Proc. Natl. Acad. Sci. USA 88:7276-7280 (Aug. 1991). cited by other. Holloway et al. An exonuclease-amplification coupled capture technique improves detection of PCR product. Nucleic Acids Research. 21(16):3905-3906 (1993). cited by other. Hsuih et al. Quantitative detection of HCV RNA using novel ligation-dependent polymerase chain reaction (LD-PCR). American Association for the Study of Liver Diseases. (Chicago, IL, Nov. 3-7, 1995). [poster abstract]. cited by other. Ishikawa et al. Sequence-based typing of HLA-A2 alleles using a primer with an extra base mismatch. Hum Immunol. 42(4):315-318 (1995). cited by other. James et al. Surprising fidelity of template-directed chemical ligation of oligonucleotides. Chemistry & Biology. 4:595-605 (1997). cited by other. Jiang et al. An efficient method for generation and subcloning of tandemly repeated DNA sequences with defined length, orientation and spacing. Nucl. Acids Res. 24(16):3278-3279 (1996). cited by other. Johnstone et al. Immunochemistry in Practice. (Blackwell Scientific Publications, Oxford, England, 1987) pp. 209-216 and 241-242. cited by other. Jonsson et al. Sequence of the DNA ligase-encoding gene from Thermus scotoductus and conserved motifs in DNA ligases. Gene. 151:177-180 (1995). cited by other. Kabanov et al. A new class of antivirals: antisense oligonucleotides combined with a hydrophobic substituent effectively inhibit influenze virus reproduction and synthesis of virus-specific proteins in MDCK cells. FEBS Lett. 259(2):327-330 (1990).cited by other. Kalin et al. Evaluation of the ligase chain reaction (LCR) for the detection of point mutations. Mutation Research. 283(2):119-123 (1992). cited by other. Kanaya et al. Template-Directed Polymerization of Oligoadenylates Using Cyanogen Bromide. Biochemistry. 25:7423-7430 (1986). cited by other. Kaplan et al. Rapid photolytic release of adenosine 5'-triphosphate from a protected analogue: utilization by the Na:K pump of human red blood cell ghosts. Biochem. 17:1929-1935 (1978). cited by other. Kellogg et al. TaqStart Antibody.TM.: "Hot Start" PCR facilitated by a neutralizing monoclonal antibody directed against Taq DNA polymerase. BioTechniques. 16(6):1134-1137 (1994). cited by other. Kessler. The digoxigenin: anti-dioxgenin (DIG) technology--a survey on the concept and realization of a novel bioanalytical indictator system. Mol Cell Probes. 5:161-205 (1991). cited by other. Kimpton et al. Automated DNA profiling employing multiplex amplification of short tandem repeat loci. PCR Methods and Applications. 3(1):13-22 (1993). cited by other. King et al., Bridging the gap. Joining of nonhomologous ends by DNA polymerases. Journal of Biological Chemistry. 269(18):13061-13064 (1994). cited by other. Kinoshita et al. Strand Ligation in a double-stranded DNA by T4 RNA Ligase. Chemistry Letters. 797-798 (1996). cited by other. Kool. Circular oligonucleotides: new concepts in olignucleotide design. Annual Rev Biomol Struct. 25:1-28 (1996). cited by other. Kricka. Ultrasensitive immunoassay techniques. Clin Biochem. 26(5):325-331 (1993). cited by other. Kunkel et al. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods in Enzymology. 154:367-382 (1987). cited by other. Kwoh et al. Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format. Proc. Natl. Acad. Sci. USA 86:1173-1177 (1989). cited by other. Lamture et al. Direct detection of nucleic acid hybridization on the surface of a charge coupled device. Nucleic Acids Research. 22(11):2121-2125 (1994). cited by other. Landegren et al. A ligase-mediated gene detection techique. Science. 241:1017-1080 (1988). cited by other. Landegren. Molecular mechanics of nucleic acid sequence amplification. Trends Genetics. 9(6):199-202 (1993). cited by other. Lawyer et al. High-level expression, purification, and enzymatic characterization of full-length Thermus aquaticus DNA polymerase and a truncated form deficient in 5' and 3' exonuclease activity. PCR Methods Applications. 2(4):275-287 (1993). citedby other. LeFrere et al. Towards a new predictor of AIDS progression through the quantitation of HIV-1 DNA copies by PCR in HIV-infected individuals. British Journals of Haematology. 82(2):467-471 (1992). cited by other. Letsinger et al. Cholesteryl-conjugated oligonucleotides: synthesis, properties, and activity as inhibitors of replication of human immunodeficiency virus in cell culture. Proc Natl Acad Sci USA. 86:6553-6556 (1989). cited by other. Letsinger et al. Synthesis of thymidine oligonculeotides by phosphite triester intermediates. J Am Chem Soc. 98(12):3655-3661 (Jun. 9, 1976). cited by other. Lichter et al. High-resolution mapping of human chromosome 11 by in situ hybridization with cosmid clones. Science. 247:64-69 (1990). cited by other. Little, Strand Displacement Amplification and Homogeneous Real-Time Detection Incorporated in a Second-Generation DNA Probe System, BDProbeTecET. Clin. Chem. 45:777-784 (1999). cited by other. Liu et al. Rolling Cycle DNA Synthesis: Small Circular Oligonucleotides as Efficient Templates for DNA Polymerases. J. Am. Chem. Soc. 118:1587-1594 (1996). cited by other. Lizardi et al. Cascade rolling circle amplification, a homogeneous fluorescence detection system for DNA diagnostics. Clinical Chemistry 43(11):2219-2220 (1997). cited by other. Lockhart et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology. 14:1675-1680. (1996). cited by other. Lu et al. High concentration of peripherial blood mononuclear cells harboring infectious virus correlates with rapid progression of human immunodeficiency virus Type1-related diseases. JID 168(5):1165-1168 (1993). cited by other. Lukyanov et al. Molecule by molecule PCR amplification of complex DNA mixtures for direct sequencing: an approach to in vitro cloning. Nucleic Acids Research. 24(11):2194-2195 (1996). cited by other. Luo et al. Improving the fidelity of Thermus thermophilus DNA ligase. Nucl Acids Res. 24(14):3071-3078 (1996). cited by other. Lyons et al. Immunosuppressant FK506 promotes neurite outgrowth in cultures of PC12 cells and sensory ganglia. Proc Natl Acad Sci U S A. 91(8):3191-3195 (1994). cited by other. Manoharan et al. Chemical modifications to improve uptake and bioavailability of antisense oligonucleotides. Ann NY Acad Sci. 660:306-309 (1992). cited by other. Manoharan et al. Cholic acid-oligonucleotide conjugates for antisense applications. Bioorg Med Chem Let. 4(8):1053-1060 (1994). cited by other. Manoharan et al. Introduction of a lipophilic thioether tether in the minor groove of nucleic acids for antisense applications. Biorg Med Chem Let. 3(12):2765-2770 (1993). cited by other. Manoharan et al. Lipidic nucleic acids. Tetra Lett. 36(21):3651-3654 (1995). cited by other. Manoharan et al. Oligonucleotide conjugates: alteration of the pharmacokinetic properties of antisense agents. Nucleoside & Nucleotides. 14:969-973 (1995). cited by other. Marshall et al. A biopolymer by an other name would bind as well: a comparison of the ligand-binding pockets of nucleic acids and proteins. Structure. 5(6):729-734. (1997). cited by other. Marshall et al. Detection of HCV RNA by the asymmetric gap ligase chain reaction. PCR Methods and Applications. 4:80-84 (1994). cited by other. Maskos et al. Oligonucleotide hybridizations on glass supports: a novel linker for oligonucleotide synthesized in situ. Nucleic Acids Research. 20(7):1679-1684 (1992). cited by other. McCray et al. A new approach to time-resolved studies of ATP-requiring biological systems: laser flash photolysis of caged ATP. Proc Natl Acad Sci USA. 77(12):7237-7241 (1980). cited by other. Melton et al. Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Research. 12(18):7035-7056 (1984). cited by other. Mendoza et al. High-Throughput Microarray-Based Enzyme-Linked Immunosorbent Assay (ELISA). BioTechniques. vol. 27(4):778-788 (1999). cited by other. Metzker et al. Termination of DNA synthesis of novel 3'-modified-deoxyribonucleoside 5'-triphosphates. Nucleic Acids Research. 22(20):4259-4267 (1994). cited by other. Nallur et al., Signal amplification by rolling circle amplification on DNA microarrays. Nucl. Acids Res. 29:E118 (2001). cited by other. Navarro et al. A general strategy for cloning viroids and other small circular RNAs that uses nminimal amounts of template and does not require prior knowledge of its sequence. J Virol Meth. 56:59-66 (1996). cited by other. Nazerenko et al. A closed tube format for amplification and detection of DNA based on energy transfer. Nucl. Acids Res. 25:2516-2521 (Jun. 1997). cited by other. Newton et al. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucl. Acids Res. 17(7):2503-2516 (1989). cited by other. Nichols et al. A universal nucleosides for use at ambiguous sites in DNA primers. Nature. 369(6480):492-493 (1984). cited by other. Nielsen et al. Peptide nucleic acids (PNAs): potential anti-sense and anti-gene agents. Anti-Cancer Drug Design. 8:53-63 (1993). cited by other. Nikiforov et al. Genetic bit analysis: a solid phase method for typing single nucleotide polymorphisms. Nucleic Acids Research. 22(20):4167-4175 (1994). cited by other. Nikiforov et al. The use of phosphorothioate primers and exonuclease hydrolysis for the preparation of single-stranded PCR products and their detection by solid-phase hybridization. PCR Methods and Applications. 3:285-291 (1994). cited by other. Nilsson et al. Padlock probes reveal single-nucleotide differences, parent of origin and in situ distribution of centromeric sequences in human chromosomes 13 and 21. Nature Genet. 16:252-255 (1997). cited by other. Nilsson et al. Padlock probes: circularizing oligonucleotides for localized DNA detection. Science. 265:2085-2088 (1994). cited by other. Nilsson et al. Real-time monitoring of rolling-circle amplification using a modified molecular beacon design. Nucleic Acids Res. 30(14):e66 (2002). cited by other. Oberhauser et al. Effective incorporation of 2'-o-methyl-oligoribonculeotides into liposomes and enhanced cell association through modification with thiocholesterol. Nucl Acids Res. 20(3):533-538 (1992). cited by other. Orum et al. Single base pair mutation analysis by PNA directed PCR clamping. Nucleic Acids Research. 21(23):5332-5336 (1993). cited by other. Panasenko et al. A simple, three-step procedure for the large scale purification of DNA ligase from a hybrid .lamda. lysogen construction in vitro. Journal Biological Chemistry. 253(13):4590-4592 (1978). cited by other. Parker et al. Targeted gene walking polymerase chain reaction. Nucl Acids Res. 19:3055-3060 (1991). cited by other. Piatak et al. High levels of HIV-1 in plasma during all stages of infection determined by competitive PCR. Science. 259:1749-1754 (1993). cited by other. Pillai. Photoremovable protecting groups in organic synthesis. Synthesis. 1-26 (1980). cited by other. Pokrovskaya et al. In vitro transcription: preparative RNA yields in analytical scale reactions. Analytical Biochemistry. 220:420-423 (1994). cited by other. Porstmann et al. Quantitation of 5-bromo-2-deoxyuridine incorporation into DNA: an enzyme immunoassay for the assessment of the lymphoid cell proliferative response. J Immunol Meth. 82:169-179 (1985). cited by other. Prakash et al. Molecular Recongition by Circular Olignucletides. Strong Binding of Single-Stranded DNA and RNA. J Chem Soc, Chem Commun. 1161-1163 (1991). cited by other. Prakash et al. Structural effects in the recognition of DNA by circular oligonucleotides. J Amer Chem Soc. 114:3253-3527 (1992). cited by other. Prober et al. A system for rapid DNA sequencing with fluoroscent chain-terminating dideoxynucleotides. Science. 238:336-341 (1987). cited by other. Protein immobilization: fundamentals and applications, Richard F. Taylor, ed. (M. Dekker, New York, 1991). cited by other. Ramsing et al. Helix-coil transition of parallel-stranded DNA. Thermodynamics of hairpin and linear duplex oligonucleotides. Biochem. 28:9528-9535 (1989). cited by other. Reese et al. The H-phosphonate approach to the solution phase synthesis of linear and cyclic oligoribonucleotides. Nucleic Acids Research. 27(4):963-971 (1999). cited by other. Richards et al. Conditional mutator phenotypes in hMSH2-deficient tumor cell lines. Science. 277-1523-1526 (1997). cited by other. Ried et al. Simultaneous visualization of seven different DNA probes by in situ hybridization using combinational fluoroscence and digital imaging microscopy. Proc Natl Acad Sci USA. 89(4):1388-1392 (1982). cited by other. Rossi et al. Functional characterization of the T4DNA ligase: a new insight into the mechanism of action. Nucleic Acids Res. 25(11):2106-2113 (1997). cited by other. Rubin et al. Convergent DNA synthesis: a non-enzymatic diverization approach to circular oligodeoxynucleotides. Nucleic Acids Res. 23(17):3547-3553 (1995). cited by other. Rys et al. Preventing false positives: quantitative evaluation of three protocols for inactivation of polymerase chain reaction amplification products. Journal of Clinical Microbiology. 31(9):2356-2360 (1993). cited by other. Saiki et al. Enzymatic Amplification of .beta.-Globin Genomic Sequences and Restriction Site Analysis for Diagnosis of Sickle Cell Anemia. Science. 230:1350-1354 (1985). cited by other. Saiki et al. Primer-Directed Enzymatic Amplification of DNA with a Thermostable DNA Polymerase. Science 239:487-491 (Jan. 29, 1988). cited by other. Saison-Behmoaras et al. Short modified antisense oligonucleotides directed against Ha-ras point mutation induce selective cleavage of the mRNA and inhibit T24 cells proliferation. EMBO J. 10(5):1111-1118 (1991). cited by other. Saksela et al. Human immunodeficiency virus type 1 mRNA expression in peripheral blood cells predicts disease progression independently of the numbers of CD4+ lymphocytes. Proc Natl Acad Sci USA. 91(3):1104-1108 (1994). cited by other. Saris et al. Blotting of RNA onto ion exchange paper allowing subsequent characterization by in situ translation in addition to blot hybridization. Nucleic Acids Res. 10(16):4831-4843 (1982). cited by other. Schena et al. DNA Microarrays: A Practical Approach. (Oxford University Press, New York, 1999) 1-16. cited by other. Schena et al. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA. 93:10614-10619 (1994). cited by other. Schena et al. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 270:467-470 (1995). cited by other. Schenborn et al. A novel transcription property of SP6 and T7 RNA polymerases: dependence on template structure. Nucleic Acids Research. 13(17):6223-6236 (1985). cited by other. Schenk et al. The accessibility of thiophosphorylated groups in DNA fragments to the enzymatic activity of ligases and restriction endonclease Bbs 1. Biochem Mol Biol Int. 36(5):1037-1043 (1995) Abstract. cited by other. Schwartz et al. Improved yields of long PCR products using gene 32 protein. Nucl Acids Res. 18(4):1079 (1990). cited by other. Schweitzer and Kingsmore. Combining nucleic acid amplification and detection. Curr. Opin. Biotech. 12(1):21-27 (Feb. 2001). cited by other. Shea et al. Synthesis, hybridization properties and antiviral activity of lipid-oligodeoxynucleotide conjugates. Nucl Acids Res. 18(13):3777-3783 (1990). cited by other. Shumaker et al. Mutation detection by solid phase primer extension. Human Mutation. 7(4):346-354 (1996). cited by other. Silzel et al. Mass-sensing, Multianalyte Microarray Immunoassay with Imaging Detection. Clin. Chem. 44: 2036-2043 (1998). cited by other. Simpson. The natural somatic mutation frequency and human carcinogenesis. Adv Cancer Res. 71:209-240 (1997). cited by other. Skerra. Phosphorothioate primers improve the amplification of DNA sequences by DNA polymerases with proofreading activity. Nucleic Acids Res. 20(14):3551-3554 (1992). cited by other. Stratagene Catalog, p. 39 (1988). cited by other. Stratagene Catalog, p. 76 (1992). cited by other. Strauss et al. Quantitative measurement of calretinin and .beta.-actin mRNA in rat brain micropunches without prior isolation of RNA. Mol Brain Res. 20:229-239 (1993). cited by other. Strong et al. Marked improvement of PAC and BAC cloning is achieved using electroelution of pulsed-field gel-separated partial digests of genomic DNA. Nucleic Acids Res. 25(19):3959-3961 (1997). cited by other. Studier et al. Use of T7 RNA polymerase to direct expression of cloned genes. Methods in Enzymology. 185:60-89 (1990). cited by other. Stump et al., The use of modified primers to eliminate cycle sequencing artifacts. Nucl. Acids Res. 27:4642-4648 (1999). cited by other. Svinarchuk et al. Inhibition of HIV proliferation in MT-4 cells by antisense oligonucleotide conjugated to lipophilic groups. Biochimie. 75:49-54 (1993). cited by other. Syvanen et al. Fast quantification of nucleic acid hybrids by affinity-based hybrid collection. Nucleic Acids Research. 14(12):5037-5048 (1986). cited by other. Tabor et al. Selective inactivation of the exonuclease activity of bacteriohage T7 DNA polymerase by in Vitro Mutagenesis. J Biol Chem. 264(11):6447-6458 (1989). cited by other. Tabor et al. Selective oxidation of the exonuclease domain of bacteriophage T7 DNA polymerase. J Biol Chem. 262:15330-15333 (1987). cited by other. Thelwell et al. Mode of action and application of Scorpion primers to mutation detection. Nucl. Acids Res. 28(19):3752-3761 (2000). cited by other. Thomas et al. Cascade rolling circle amplification, a homogenous fluorescence detection system for DNA diagnostics. Clin Chem. 43:2119, Abs. 38 (1997). cited by other. Thorbjarnardottir et al. Cloning and sequence analysis of the DNA lligase-encoding gene of Rhodothermus marinus, and overproduction, purification and characterization of two thermophilic DNA ligases. Gene 161:1-6 (1995). cited by other. Tyagi et al. Extremely sensitive, background-free gene detection using binary probes and Q.beta. replicase. Proc. Natl Acda. Sci. USA 93:5395-5400 (1996). cited by other. Uemori et al. Cloning fo the DNA polymerase gene of Bacillus caldotenax and characterization of the gene product. J. Biochem. 113(3):401-410 (Mar. 1993). cited by other. Unrau et al. Non-cloning amplification of specific DNA fragments from whole genomic DNA digests using DNA `indexers`. Gene. .145(2):163-169 (1994). cited by other. Velculescu et al. Serial analysis of gene expression. Science. 270:484-487 (1995). cited by other. Vogelstein et al. Supercoiled loops and eucaryotic DNA replication. Cell. 22:79-85 (1980). cited by other. Voisey et al. Interrogation of multimeric DNA amplification products by competitive primer extension using bst DNA polymerase (large fragment). Biotechniques. 31(5):1122-1129 (2001). cited by other. Walker et al. Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system. Proc Natl Acad Sci USA. 89:392-396 (1992). cited by other. Walker et al. Strand displacement amplification--an isothermal, in vitro DNA amplification technique. Nucleic Acids Research. 20(7):1691-1696 (1992). cited by other. Walter et al. Strand displacement amplification as an in vitro model for rolling-circle replication: deletion formation and evolution during serial transfer. Proc Natl Acad Sci USA. 91:7937-7941 (1994). cited by other. Wang et al. Circular RNA oligonucleotides. Synthesis, nucleic acid binding properties, and a comparison with circular DNAs. Nucl. Acids Res. 22(12):2326-2333 (1994). cited by other. Welford et al. Detection of differentially expressed genes in primary tumor tissues using representational differences analysis coupled to microarray hybridization. Nucleic Acids Res. 26(12):3059-3065 (1998). cited by other. Wemmer et al. Preparation and melting of single strand circular DNA loops. Nucleic Acids Res. 13(23):8611-8621 (1985). cited by other. White et al. Concatemer chain reaction: a Taq DNA polymerase-mediated mechanism for generating long tandemly repetitive DNA sequences. Anal Biochem. 199(2):184-190 (1991). cited by other. Wiedmann et al. Ligase chain reaction (LCR)--overview and applications. PCR Methods and Applications. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1994) [pp. S51-S64]. cited by other. Wilson et al. Enzyme complex amplification-a signal amplification method for use in enzyme immunoassays. Anal Biochem. 209(1):183-187 (1993). cited by other. Winn-Deen et al. Non-radioactive detection of Mycobacterium tuberculosis LCR products in a microtitre plate format. Molecular and Cellular Probes. (England) 7(3):179-186 (1993). cited by other. Xu et al. Nonenzymatic autoligation in direct three-color detection of RNA and DNA point mutations. Nature Biotechnology. 19:148-152 (2001). cited by other. Yang et al. Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes. Nucleic Acids Res. 27(6):1517-1523 (1999). cited by other. Young et al. Quantitative analysis of solution hybridation. Nucleic Acid Hybridisation: A Practical Approach. (IRL Press, 1985) pp. 47-71. cited by other. Zehavi et al. Light sensitive glycosides. II. 2-Nitrobenzyl 6-Deoxy-.alpha.-L-mannopyranoside and 2-Nitrobenzyl 6-Deoxy-.beta.-L-galactophyranoside. J Organic Chem. 37(14):2285-2285 (1972). cited by other. Zehavi et al. Light-Sensitive Glycosides. I. 6-nitroveratryl .beta.-D-glucopyranoside and 2-nitrobenzyl .beta.-D-glucopyranoside. J Organic Chem. 37(14):2281-2285 (1972). cited by other. Zhang et al. Amplification of target-specific, ligation-dependent circular probe. Gene 211:277-285 (1990). cited by other. Zhang et al. Whole genome amplification from a single cell: Implications for genetic analysis. Proc. Natl. Acad. Sci. USA 89:5847-5851 (Jul. 1992). cited by other. Zhu et al. Global Analysis of Protein Activities Using Proteome Chips. Science 293(5537):2101-2105 (2001). cited by other. Aliotta et al. Thermostable Bst DNA polymerase I lacks a 3'.fwdarw. .ident.' proofreading exonuclease activity. Genet. Anal (Netherlands) 12:185-195 (1996). cited by other. Anderson and Seilhamer. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18:533-537 , (1997). cited by other. Beaucage et al. Deoxynucleoside Phosphoramidites-A New Class of Key Intermediates For Deoxypolycleotide Synthesis. Tetrahedron Lett. 22:1850 (1981). cited by other. Chatterjee et al. Cloning and overexpression of the gene encoding bacteriophage T5 DNA polymerase. Gene 97:13-19 (1991). cited by other. Abravaya et al. Detection of point mutations with a modified ligase chain reaction (Gap-LCR). Nucleic Acids Res. 23(4):675-682 (1995). cited by other. U.S. Appl. No. 09/803,713, Alsmadi et al., filed Mar. 9, 2001, Issue Notification, May 14, 2003. cited by other. U.S. Appl. No. 09/803,713, Alsmadi et al., filed Mar. 9, 2001, Notice of Allowance, Feb. 4, 2003. cited by other. U.S. Appl. No. 09/803,713, Alsmadi et al., filed Mar. 9, 2001, Supplemental Response, Jan. 23, 2003. cited by other. U.S. Appl. No. 09/803,713, Alsmadi et al., filed Mar. 9, 2001, Response after Non-Final Action, Nov. 5, 2002. cited by other. U.S. Appl. No. 09/803,713, Alsmadi et al., filed Mar. 9, 2001, Non-Final Rejection, Jun. 5, 2002. cited by other. U.S. Appl. No. 09/803,713, Alsmadi et al., filed Mar. 9, 2001, Response to Election / Restriction Filed, Mar. 29, 2002. cited by other. U.S. Appl. No. 09/803,713, Alsmadi et al., filed Mar. 9, 2001, Restriction Requirement, Feb. 21, 2002. cited by other. U.S. Appl. No. 10/325,490, Alsmadi et al., filed Dec. 19, 2002, Abandonment for Failure to Respond to Office Action, Mar. 8, 2007. cited by other. U.S. Appl. No. 10/325,490, Alsmadi et al., filed Dec. 19, 2002, Non-Final Rejection, Aug. 9, 2006. cited by other. U.S. Appl. No. 10/325,490, Alsmadi et al., filed Dec. 19, 2002, Response after Non-Final Action, May 25, 2006. cited by other. U.S. Appl. No. 10/325,490, Alsmadi et al., filed Dec. 19, 2002, Non-Final Rejection, Jan. 24, 2006. cited by other. U.S. Appl. No. 10/325,490, Alsmadi et al., filed Dec. 19, 2002, Response to Election / Restriction Filed, Oct. 21, 2005. cited by other. U.S. Appl. No. 10/325,490, Alsmadi et al., filed Dec. 19, 2002, Restriction Requirement, Sep. 16, 2005. cited by other. U.S. Appl. No. 10/404,944, Alsmadi et al., filed Mar. 31, 2003, Abandonment for Failure to Respond to Office Action, Nov. 27, 2006. cited by other. U.S. Appl. No. 10/404,944, Alsmadi et al., filed Mar. 31, 2003, Non-Final Rejection, May 9, 2006. cited by other. U.S. Appl. No. 10/404,944, Alsmadi et al., filed Mar. 31, 2003, Response after Non-Final Action, Mar. 6, 2006. cited by other. U.S. Appl. No. 10/404,944, Alsmadi et al., filed Mar. 31, 2003, Non-Final Rejection, Dec. 5, 2005. cited by other. U.S. Appl. No. 09/547,757, Faruqi, filed Apr. 12, 2000, Issue Notification, Mar. 21, 2002. cited by other. U.S. Appl. No. 09/547,757, Faruqi, filed Apr. 12, 2000, Notice of Allowance, Aug. 31, 2001. cited by other. U.S. Appl. No. 09/597,836, Kingsmore et al., filed Jun. 20, 2000, Issue Notification, Feb. 20, 2003. cited by other. U.S. Appl. No. 09/597,836, Kingsmore et al., filed Jun. 20, 2000, Notice of Allowance, Nov. 17, 2002. cited by other. U.S. Appl. No. 09/597,836, Kingsmore et al., filed Jun. 20, 2000, RCE with Response to Office Action, Sep. 18, 2002. cited by other. U.S. Appl. No. 09/597,836, Kingsmore et al., filed Jun. 20, 2000, Final Rejection, Mar. 19, 2002. cited by other. U.S. Appl. No. 09/597,836, Kingsmore et al., filed Jun. 20, 2000, Response after Non-Final Action, Feb. 6, 2002. cited by other. U.S. Appl. No. 09/597,836, Kingsmore et al., filed Jun. 20, 2000, Non-Final Rejection, Nov. 5, 2001. cited by other. U.S. Appl. No. 09/597,836, Kingsmore et al., filed Jun. 20, 2000, Response after Non-Final Action, Sep. 20, 2001. cited by other. U.S. Appl. No. 09/597,836, Kingsmore et al., filed Jun. 20, 2000, Non-Final Rejection, Mar. 20, 2001. cited by other. U.S. Appl. No. 09/597,836, Kingsmore et al., filed Jun. 20, 2000, Preliminary Amendment, Oct. 26, 2000. cited by other. U.S. Appl. No. 10/341,287, Kingsmore et al., filed Jan. 13, 2003, Post Issue Communication - Certificate of Correction, Sep. 7, 2005. cited by other. U.S. Appl. No. 10/341,287, Kingsmore et al., filed Jan. 13, 2003, Request for Certificate of Correction, Aug. 25, 2005. cited by other. U.S. Appl. No. 10/341,287, Kingsmore et al., filed Jan. 13, 2003, Issue Notification, Jul. 6, 2005. cited by other. U.S. Appl. No. 10/341,287, Kingsmore et al., filed Jan. 13, 2003, Notice of Allowance, Mar. 15, 2005. cited by other. U.S. Appl. No. 10/341,287, Kingsmore et al., filed Jan. 13, 2003, Response after Non-Final Action, Jan. 4, 2005. cited by other. U.S. Appl. No. 10/341,287, Kingsmore et al., filed Jan. 13, 2003, Terminal Disclaimer Filed, Jan. 4, 2005. cited by other. U.S. Appl. No. 10/341,287, Kingsmore et al., filed Jan. 13, 2003, Non-Final Rejection, Oct. 22, 2004. cited by other. U.S. Appl. No. 11/187,537, Kingsmore et al., filed Jul. 22, 2005, Miscellaneous Communication to Applicant Notice of Defective Declaration, Oct. 4, 2007. cited by other. U.S. Appl. No. 11/187,537, Kingsmore et al., filed Jul. 22, 2005, Petition Decision - Granted, Mar. 2, 2006. cited by other. U.S. Appl. No. 11/187,537, Kingsmore et al., filed Jul. 22, 2005, Petition Entered, Dec. 23, 2005. cited by other. U.S. Appl. No. 09/897,259, Ward et al., filed Jul. 2, 2001, Issue Notification, Jan. 15, 2004. cited by other. U.S. Appl. No. 09/897,259, Ward et al., filed Jul. 2, 2001, Examiner's Amendment, Dec. 8, 2003. cited by other. U.S. Appl. No. 09/897,259, Ward et al., filed Jul. 2, 2001, Notice of Allowance, Jul. 1, 2003. cited by other. U.S. Appl. No. 09/897,259, Ward et al., filed Jul. 2, 2001, Response after Non-Final Action, Apr. 18, 2003. cited by other. U.S. Appl. No. 09/897,259, Ward et al., filed Jul. 2, 2001, Non-Final Rejection, Jan. 17, 2003. cited by other. U.S. Appl. No. 09/897,259, Ward et al., filed Jul. 2, 2001, Response to Election / Restriction Filed, Nov. 4, 2002. cited by other. U.S. Appl. No. 09/897,259, Ward et al., filed Jul. 2, 2001, Restriction Requirement, Sep. 30, 2002. cited by other. U.S. Appl. No. 09/910,383, Nailur et al., filed Jul. 20, 2001, Abandonment for Failure to Respond to Office Action, Nov. 14, 2007. cited by other. U.S. Appl. No. 09/910,383, Nailur et al., filed Jul. 20, 2001, Advisory Action, May 1, 2007. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Amendment/Argument after Notice of Appeal, Apr. 18, 2007. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Notice of Appeal Filed, Apr. 18, 2007. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Examiner Interview Summary, Apr. 9, 2007. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Final Rejection, Dec. 13, 2006. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Response after Non-Final Action, Oct. 2, 2006. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Non-Final Rejection, Jun. 15, 2006. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Withdrawal of Informal Amendment Notice, Apr. 7, 2006. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Response after Non-Final Action, Mar. 22, 2006. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Notice of Informal or Non-Responsive RCE Amendment, Mar. 27, 2006. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Advisory Action, Dec. 13, 2005. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Amendment after Final Rejection, Nov. 23, 2005. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Examiner Interview Summary Record, Oct. 12, 2005. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Advisory Action, Sep. 14, 2005. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Amendment after Final Rejection, Aug. 26, 2005. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Final Rejection, May 23, 2005. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Response after Non-Final Action, Mar. 14, 2005. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Non-Final Rejection, Jan. 27, 2005. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Response after Non-Final Action, Nov. 22, 2004. cited by other. U.S. Appl. No. 09/910,383, Nallur et al., filed Jul. 20, 2001, Non-Final Rejection, Jun. 23, 2004. cited by other. U.S. Appl. No. 09/977,868, Dean et al., filed Oct. 15, 2001, Issue Notification, Nov. 30, 2005. cited by other. U.S. Appl. No. 09/977,868, Dean et al., filed Oct. 15, 2001,Notice of Allowance, Feb. 22, 2005. cited by other. U.S. Appl. No. 09/977,868, Dean et al., filed Oct. 15, 2001, Examiner's Amendment, Feb. 22, 2005. cited by other. U.S. Appl. No. 09/977,868, Dean et al., filed Oct. 15, 2001, Response after Non-Final Action, Jan. 4, 2005. cited by other. U.S. Appl. No. 09/977,868, Dean et al., filed Oct. 15, 2001, Non-Final Rejection, Sep. 9, 2004. cited by other. U.S. Appl. No. 09/977,868, Dean et al., filed Oct. 15, 2001, Preliminary Amendment, Apr. 11, 2002. cited by other. U.S. Appl. No. 09/982,212, Dean et al., filed Oct. 18, 2001, Issue Notification, Aug. 21, 2003. cited by other. U.S. Appl. No. 09/982,212, Dean et al., filed Oct. 18, 2001, Notice of Allowance, May 20, 2003. cited by other. U.S. Appl. No. 09/982,212, Dean et al., filed Oct. 18, 2001, Response after Non-Final Action, May 7, 2003. cited by other. U.S. Appl. No. 09/982,212, Dean et al., filed Oct. 18, 2001, Non-Final Rejection, Apr. 18, 2003. cited by other. U.S. Appl. No. 09/982,212, Dean et al., filed Oct. 18, 2001, Preliminary Amendment, Jan. 24, 2002. cited by other. U.S. Appl. No. 09/982,212, Dean et al., filed Oct. 18, 2001, Preliminary Amendment, Oct. 8, 2001. cited by other. U.S. Appl. No. 10/272,465, Dean et al., filed Oct. 15, 2002, Decision on Petition to Revive, May 22, 2006. cited by other. U.S. Appl. No. 10/275,465, Dean et al., filed Oct. 15, 2002, Petition to Revive Application, Mar. 16, 2006. cited by other. U.S. Appl. No. 10/272,465, Dean et al., filed Oct. 15, 2002, Issue Notification, Jun. 21, 2006. cited by other. U.S. Appl. No. 10/272,465, Dean et al., filed Oct. 15, 2002, Notice of Allowance, Dec. 13, 2005. cited by other. U.S. Appl. No. 10/272,465, Dean et al., filed Oct. 15, 2002, Examiner's Amendment, Dec. 13, 2005. cited by other. U.S. Appl. No. 10/272,465, Dean et al., filed Oct. 15, 2002, Terminal Disclaimer Filed, Sep. 6, 2005. cited by other. U.S. Appl. No. 10/272,465, Dean et al., filed Oct. 15, 2002, Response after Non-Final Action, Sep. 6, 2005. cited by other. U.S. Appl. No. 10/272,465, Dean et al., filed Oct. 15, 2002, Non-Final Rejection, Aug. 5, 2005. cited by other. U.S. Appl. No. 10/429,229, Bomarth et al., filed May 2, 2003, Issue Notification, Oct. 31, 2007. cited by other. U.S. Appl. No. 10/429,229, Bomarth et al., filed May 2, 2003, Issue Fee Payment Received, Sep. 17, 2007. cited by other. U.S. Appl. No. 10/429,229, Bomarth et al., filed May 2, 2003, Supplemental Notice of Allowance, Jul. 31, 2007. cited by other. U.S. Appl. No. 10/429,229, Bomarth et al., filed May 2, 2003, Notice of Allowance, Jun. 18, 2007. cited by other. U.S. Appl. No. 10/429,229, Bomarth et al., filed May 2, 2003, Examiner Interview Summary, Jun. 18, 2007. cited by other. U.S. Appl. No. 10/429,229, Bomarth et al., filed May 2, 2003, Examiner's Amendment, Jun. 18, 2007. cited by other. U.S. Appl. No. 10/429,229, Bomarth et al., filed May 2, 2003, Amendment after Final Rejection, Jun. 5, 2007. cited by other. U.S. Appl. No. 10/429,229, Bomarth et al., filed May 2, 2003, Final Rejection, Feb. 28, 2007. cited by other. U.S. Appl. No. 10/429,229, Bomarth et al., filed May 2, 2003, Response after Non-Final Action & Terminal Disclaimer, Dec. 18, 2006. cited by other. U.S. Appl. No. 10/429,229, Bomarth et al., filed May 2, 2003, Non-Final Rejection, Jun. 20, 2006. cited by other. U.S. Appl. No. 10/429,229, Bomarth et al., filed May 2, 2003, Response to Election / Restriction Filed, Apr. 21, 2006. cited by other. U.S. Appl. No. 10/429,229, Bomarth et al., filed May 2, 2003, Restriction Requirement, Feb. 16, 2006. cited by other. U.S. Appl. No. 11/871,707, Bomarth et al., filed Oct. 12, 2007, Notice of Publication, Jun. 5, 2008. cited by other. U.S. Appl. No. 11/871,707, Bornarth et al., filed Oct. 12, 2007, Preliminary Amendment, Jan. 31, 2008. cited by other. U.S. Appl. No. 08/754,681, Lizardi et al., filed Nov. 21, 1996, Issue Notification, Oct. 20, 2000. cited by other. U.S. Appl. No. 08/754,681, Lizardi et al., filed Nov. 21, 1996, Issue Fee Payment Verified, Jun. 23, 2000. cited by other. U.S. Appl. No. 08/754,681, Lizardi et al., filed Nov. 21, 1996, Notice of Allowance, Mar. 28, 2000. cited by other. U.S. Appl. No. 08/754,681, Lizardi et al., filed Nov. 21, 1996, Notice of Appeal Filed, Feb. 7, 2000. cited by other. U.S. Appl. No. 08/754,681, Lizardi et al., filed Nov. 21, 1996, Amendment after Final Rejection & Terminal Disclaimer Filed, Dec. 30, 1999. cited by other. U.S. Appl. No. 08/754,681, Lizardi et al., filed Nov. 21, 1996, Final Rejection, Aug. 4, 1999. cited by other. U.S. Appl. No. 08/754,681, Lizardi et al., filed Nov. 21, 1996, Supplemental Response, Apr. 16, 1999. cited by other. U.S. Appl. No. 08/754,681, Lizardi et al., filed Nov. 21, 1996, Response after Non-Final Action, Apr. 6, 1999. cited by other. U.S. Appl. No. 08/754,681, Lizardi et al., filed Nov. 21, 1996, Non-Final Rejection, Oct. 1, 1998. cited by other. U.S. Appl. No. 08/754,681, Lizardi et al., filed Nov. 21, 1996, Response after Non-Final Action, Jul. 9, 1998. cited by other. U.S. Appl. No. 08/754,681, Lizardi et al., filed Nov. 21, 1996, Non-Final Rejection, Jan. 6, 1998. cited by other. U.S. Appl. No. 08/754,681, filed Nov. 21, 1996, Response after Non-Final Action, Oct. 24, 1997. cited by other. U.S. Appl. No. 09/602,428, Lizardi et al., filed Jun. 23, 2000, Issue Notification, Nov. 21, 2001. cited by other. U.S. Appl. No. 09/602,428, Lizardi et al., filed Jun. 23, 2000, Notice of Allowance, Jun. 28, 2001. cited by other. U.S. Appl. No. 09/602,428, Lizardi et al., filed Jun. 23, 2000, Terminal Disclaimer Filed, Apr. 12, 2001. cited by other. U.S. Appl. No. 09/602,428, Lizardi et al., filed Jun. 23, 2000, Response after Non-Final Action, Apr. 12, 2001. cited by other. U.S. Appl. No. 09/602,428, Lizardi et al., filed Jun. 23, 2000, Non-Final Rejection, Nov. 22, 2000. cited by other. U.S. Appl. No. 09/602,428, Lizardi et al., filed Jun. 23, 2000, Preliminary Amendment, Jun. 23, 2000. cited by other. U.S. Appl. No. 09/841,513, Lizardi, filed Apr. 24, 2001, Issue Notification, Sep. 25, 2003. cited by other. U.S. Appl. No. 09/841,513, Lizardi, filed Apr. 24, 2001, Terminal Disclaimer Filed, May 7, 2003. cited by other. U.S. Appl. No. 09/841,513, Lizardi, filed Apr. 24, 2001, Notice of Allowance, Jan. 16, 2003. cited by other. U.S. Appl. No. 09/841,513, Lizardi, filed Apr. 24, 2001, Terminal Disclaimer Filed, Oct. 24, 2002. cited by other. U.S. Appl. No. 09/841,513, Lizardi, filed Apr. 24, 2001, Response after Non-Final Action, Oct. 24, 2002. cited by other. U.S. Appl. No. 09/841,513, Lizardi, filed Apr. 24, 2001, Non-Final Rejection, Apr. 30, 2002. cited by other. U.S. Appl. No. 09/841,513, Lizardi, filed Apr. 24, 2001, Preliminary Amendment, Apr. 24, 2001. cited by other. U.S. Appl. No. 10/413,041, Lizardi et al., filed Apr. 10, 2003, Abandonment for Failure to Respond to Office Action, Apr. 5, 2006. cited by other. U.S. Appl. No. 10/413,041, Lizardi et al., filed Apr. 10, 2003, Restriction Requirement, Sep. 22, 2005. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Issue Notification, Nov. 25, 2004. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Notice of Allowance, Jul. 14, 2004. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Amendment after Final Rejection, Jun. 17, 2004. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Examiner Interview Summary, May 25, 2004. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Final Rejection, Feb. 13, 2004. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Response after Non-Final Action, Nov. 24, 2003. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Non-Final Rejection, May 19, 2003. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Response after Non-Final Action, Jan. 14, 2003. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Non-Final Rejection, Sep. 4, 2002. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Request for Continued Examination (RCE), Jun. 17, 2002. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Notice of Appeal Filed, Jan. 25, 2002. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Final Rejection, Jul. 17, 2001. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Response after Non-Final Action, May 23, 2001. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Non-Final Rejection, Nov. 20, 2000. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Response to Election / Restriction Filed, Oct. 3, 2000. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Notice of Restarted Response Period, Jun. 30, 2000. cited by other. U.S. Appl. No. 09/460,078, Hafner et al., filed Dec. 14, 1999, Restriction Requirement, May 23, 2000. cited by other. U.S. Appl. No. 10/917,580, Hafner et al., filed Aug. 13, 2004, Issue Notification, Mar. 26, 2008. cited by other. U.S. Appl. No. 10/917,580, Hafner et al., filed Aug. 13, 2004, Notice of Allowance, Nov. 30, 2007. cited by other. U.S. Appl. No. 10/917,580, Hafner et al., filed Aug. 13, 2004, Examiner's Amendment Communication, Nov. 30, 2007. cited by other. U.S. Appl. No. 10/917,580, Hafner et al., filed Aug. 13, 2004, Terminal Disclaimer Filed, Oct. 1, 2007. cited by other. U.S. Appl. No. 10/917,580, Hafner et al., filed Aug. 13, 2004, Response after Non-Final Action, Oct. 1, 2007. cited by other. U.S. Appl. No. 10/917,580, Hafner et al., filed Aug. 13, 2004, Non-Final Rejection, Jun. 25, 2007. cited by other. U.S. Appl. No. 10/917,580, Hafner et al., filed Aug. 13, 2004, Response to Election / Restriction Filed, May 10, 2007. cited by other. U.S. Appl. No. 10/917,580, Hafner et al., filed Aug. 13, 2004, Restriction Requirement, Jan. 11, 2007. cited by other. U.S. Appl. No. 10/917,580, Hafner et al., filed Aug. 13, 2004, Preliminary Amendment, Nov. 19, 2004. cited by other. U.S. Appl. No. 10/325,665, Alsmadi et al., filed Dec. 19, 2002, Non-Final Rejection, Apr. 17, 2008. cited by other. U.S. Appl. No. 10/325,665, Alsmadi et al., filed Dec. 19, 2002, Examiner Interview Summary, Apr. 17, 2008. cited by other. U.S. Appl. No. 10/325,665, Alsmadi et al., filed Dec. 19, 2002, Non-Final Rejection, Oct. 25, 2007. cited by other. U.S. Appl. No. 10/325,665, Alsmadi et al., filed Dec. 19, 2002, Amendment / Argument after Notice of Appeal, Sep. 25, 2007. cited by other. U.S. Appl. No. 10/325,665, Alsmadi et al., filed Dec. 19, 2002, Final Rejection, Mar. 26, 2007. cited by other. U.S. Appl. No. 10/325,665, Alsmadi et al., filed Dec. 19, 2002, Response after Non-Final Action, Dec. 22, 2006. cited by other. U.S. Appl. No. 10/325,665, Alsmadi et al., filed Dec. 19, 2002, Non-Final Rejection, Aug. 3, 2006. cited by other. U.S. Appl. No. 10/325,665, Alsmadi et al., filed Dec. 19, 2002, Response after Non-Final Action & Terminal Disclaimer, Apr. 18, 2006. cited by other. U.S. Appl. No. 10/325,665, Alsmadi et al., filed Dec. 19, 2002, Non-Final Rejection, Dec. 30, 2005. cited by other. U.S. Appl. No. 10/325,665, Alsmadi et al., filed Dec. 19, 2002, Response to Electron / Restriction Filed, Sep. 21, 2005. cited by other. U.S. Appl. No. 10/325,665, Alsmadi et al., filed Dec. 19, 2002, Restriction Requirement, Apr. 21, 2005. cited by other. U.S. Appl. No. 10/335,573, Kumar et al., filed Dec. 31, 2002, Issue Notification, Nov. 30, 2005. cited by other. U.S. Appl. No. 10/335,573, Kumar et al., filed Dec. 31, 2002, Notice of Allowance, Mar. 29, 2005. cited by other. U.S. Appl. No. 10/335,573, Kumar et al., filed Dec. 31, 2002, Response after Non-Final Action, Dec. 1, 2004. cited by other. U.S. Appl. No. 10/335,573, Kumar et al., filed Dec. 31, 2002, Non-Final Rejection, Jul. 29, 2004. cited by other. U.S. Appl. No. 11/201,339, Abstract: Disclosed are compositions and methods for detecting small quantities of analytes such as proteins and peptides. The method involves associating a DNA circle with the analyte and subsequent release and rolling circle replication of the circular DNA molecule. In the method, an amplification target circle is associated with analytes using a conjugate of the circle and a specific binding molecule that is specific for the analyte to be detected. Amplification target circles not associated with the proteins are removed, the amplification target circles that are associated with the proteins are decoupled from the specific binding molecule and amplified by rolling circle amplification. The amplification is isothermic and can result in the production of a large amount of nucleic acid from each primer. The amplified DNA serves as a readily detectable signal for the analytes. Claim: We claim: 1. A method for detecting one or more analytes, the method comprising (a) bringing into contact one or more analyte samples and one or more reporter binding molecules, wherein eachreporter binding molecule comprises a specific binding molecule and an amplification target circle, wherein each specific binding molecule interacts with an analyte directly or indirectly, incubating the analyte samples and the reporter binding moleculesunder conditions that promote interaction of the specific binding molecules and analytes, and separating the specific binding molecules that interact with the analytes from the specific binding molecules that do not interact with the analytes, (b)decoupling the amplification target circles associated with the analytes from the specific binding molecules, (c) bringing into contact the decoupled amplification target circles and one or more rolling circle replication primers, wherein theamplification target circles each comprise a single-stranded, circular DNA molecule comprising a primer complement portion, wherein the primer complement portion is complementary to at least one of the rolling circle replication primers, and incubatingthe rolling circle replication primers and amplification target circles under conditions that promote hybridization between the amplification target circles and the rolling circle replication primers, (d) incubating the rolling circle replication primersand amplification target circles under conditions that promote replication of the amplification target circles, wherein replication of the amplification target circles results in the formation of tandem sequence DNA, wherein detection of tandem sequenceDNA indicates the presence of the corresponding analytes. 2. The method of claim 1, wherein at least one of the reporter binding molecules further comprises a circle capture probe, wherein the amplification target circle of the reporter binding molecule is associated with the reporter binding moleculevia a non-covalent interaction with the circle capture probe. 3. The method of claim 2, wherein the non-covalent interaction is base pairing. 4. The method of claim 3, wherein decoupling of the amplification target circle is accomplished by disrupting the base pairing. 5. The method of claim 4, wherein the base pairing is disrupted by heating the reporter binding molecules. 6. The method of claim 2, wherein the circle capture probe comprises an oligonucleotide. 7. The method of claim 6, wherein the oligonucleotide cannot be extended. 8. The method of claim 7, wherein the oligonucleotide comprises a 3' end and a 5' end, wherein only the 5' end is free. 9. The method of claim 8, wherein the oligonucleotide is coupled to the specific binding molecule of the reporter binding molecule via the 3' end of the oligonucleotide. 10. The method of claim 8, wherein the 3' end of the oligonucleotide is blocked. 11. The method of claim 7, wherein the oligonucleotide is blocked. 12. The method of claim 1, wherein at least one of the reporter binding molecules further comprises a circle linker, wherein the amplification target circle of the reporter binding molecule is coupled to the reporter binding molecule via thecircle linker. 13. The method of claim 12, wherein the circle linker comprises a cleavable bond. 14. The method of claim 13, wherein decoupling of the amplification target circle is accomplished by cleaving the cleavable bond. 15. The method of claim 14, wherein the cleavable bond is cleaved by treatment with a reducing agent. 16. The method of claim 15, wherein the cleavable bond is a disulfide bond. 17. The method of claim 16, wherein the circle linker comprises dithiobis succinimidyl propionate, dimethyl 3,3'-dithiobispropionimidate, dithio-bis-maleimidoethane, 3,3'-dithiobis sulfosuccinimidyl propionate, succinimidyl6-[3-(2-pyridyldithio)-propionamido]hexonate, or N-succinimidyl 3-[2-pyridyldithio]propionate. 18. The method of claim 14, wherein the cleavable bond is cleaved by treatment with periodate. 19. The method of claim 18, wherein the cleavable bond is a dihydroxy bond. 20. The method of claim 19, wherein the circle linker comprises 1,4bis-maleimidyl-2,3-dihydroxybutane, disuccinimidyl tartrate, or disulfosuccinimidyl tartrate. 21. The method of claim 12, wherein the circle linker is coupled to the amplification target circle via a reactive group on the amplification target circle. 22. The method of claim 21, wherein the reactive group is an allyl amino group. 23. The method of claim 1, wherein a plurality of reporter binding molecules are brought into contact with the one or more analyte samples. 24. The method of claim 1, wherein a plurality of analyte samples are brought into contact with the one or more reporter binding molecules. 25. The method of claim 1, wherein at least one of the analytes is a protein or peptide. 26. The method of claim 1, wherein at least one of the analytes is a lipid, glycolipid, or proteoglycan. 27. The method of claim 1, wherein at least one of the analytes is from a human source. 28. The method of claim 1, wherein at least one of the analytes is from a non-human source. 29. The method of claim 1, wherein none of the analytes are nucleic acids. 30. The method of claim 1, wherein the specific binding molecules that interact with the analytes are separated by bringing into contact at least one of the analyte samples and one or more analyte capture agents, wherein each analyte captureagent interacts with an analyte directly or indirectly, wherein at least one analyte, if present in the analyte sample, interacts with at least one analyte capture agent, and separating analyte capture agents from the analyte samples, thus separatingspecific binding molecules that interact with the analytes from the analyte samples. 31. The method of claim 30, wherein at least one analyte capture agent is associated with a solid support, wherein analytes that interact with the analyte capture agent associated with a solid support become associated with the solid support. 32. The method of claim 31, wherein the solid support comprise one or more reaction chambers, wherein a plurality of the analyte capture agents are located in the same reaction chamber on the solid support. 33. The method of claim 31, wherein a plurality of reporter binding molecules are brought into contact with one or more analyte samples, wherein two or more of the amplification target circles are replicated in the same reaction chamber of thesolid support, wherein the amplification target circles replicated in the same reaction chamber of the solid support are different, wherein each different amplification target circle produces a different tandem sequence DNA, wherein the presence orabsence of different analytes is indicated by the presence or absence of corresponding tandem sequence DNA. 34. The method of claim 33, wherein replication of each different amplification target circle is primed by a different one of the rolling circle replication primers. 35. The method of claim 31, wherein the solid support comprises acrylamide, agarose, cellulose, cellulose, nitrocellulose, glass, gold, polystyrene, polyethylene vinyl acetate, polypropylene, polymethacrylate, polyethylene, polyethylene oxide,glass, polysilicates, polycarbonates, teflon, fluorocarbons, nylon, silicon rubber, polyanhydrides, polyglycolic acid, polylactic acid, polyorthoesters, functionalized silane, polypropylfumerate, collagen, glycosaminoglycans, or polyamino acids. 36. The method of claim 30, further comprising bringing into contact at least one of the analyte samples and at least one of the reporter binding molecules with at least one accessory molecule, wherein the accessory molecule affects theinteraction of at least one of the analytes and at least one of the specific binding molecules or at least one of the analyte capture agents. 37. The method of claim 36, wherein the accessory molecule is brought into contact with at least one of the analyte samples, at least one of the reporter binding molecules, or both, prior to, simultaneous with, or following step (a). 38. The method of claim 36, wherein at least one analyte capture agent is associated with a solid support, wherein the accessory molecule is associated with the solid support. 39. The method of claim 38, wherein the accessory molecule is associated with the solid support by bringing the accessory molecule into contact with the solid support prior to, simultaneous with, or following step (a). 40. The method of claim 36, wherein the accessory molecule is a protein kinase, a protein phosphatase, an enzyme, or a compound. 41. The method of claim 36, wherein the accessory molecule is a molecule of interest, wherein one or more of the analytes are test molecules, wherein interactions of the test molecules with the molecule of interest are detected. 42. The method of claim 36, wherein at least one of the analytes is a molecule of interest, wherein the accessory molecule is a test molecule, wherein interactions of the test molecule with the molecule of interest are detected. 43. The method of claim 30, wherein the analyte samples include one or more first analyte samples and one or more second analyte samples, wherein the reporter binding molecules include one or more first reporter binding molecules and one ormore second reporter binding molecules, the method further comprising, following step (a) and prior to bringing the analyte samples and the solid support into contact, mixing one or more of the first analyte samples and one or more of the second analytesamples, wherein for each first reporter binding molecule there is a matching second reporter binding molecule, wherein the specific binding molecules of the first reporter binding molecules interacts with the same analyte as the specific bindingmolecules of the matching second reporter binding molecule, wherein the amplification target circle of each different reporter binding molecule is different, wherein each different amplification target circle produces a different tandem sequence DNA,wherein the presence or absence of the same analyte in different analyte samples is indicated by the presence or absence of corresponding tandem sequence DNA. 44. The method of claim 43, wherein replication of each different amplification target circle is primed by a different one of the rolling circle replication primers. 45. The method of claim 44, wherein the tandem sequence DNA corresponding to one of the analytes and produced in association with a first reporter binding molecule is in the same location on the solid support as tandem sequence DNAcorresponding to the same analyte and produced in association with the matching second reporter binding molecule, wherein the presence or absence of the same analyte in different analyte samples is indicated by the presence or absence of correspondingtandem sequence DNA. 46. The method of claim 30, wherein at least one of the analyte capture agents is a molecule of interest, wherein one or more of the analytes are test molecules, wherein interactions of the test molecules with the molecule of interest aredetected. 47. The method of claim 30, wherein at least one of the analytes is a molecule of interest, wherein one or more of the analyte capture agents are test molecules, wherein interactions of the test molecules with the molecule of interest aredetected. 48. The method of claim 1, wherein a plurality of reporter binding molecules are brought into contact with one or more analyte samples, wherein two or more of the amplification target circles are replicated in the same reaction, wherein theamplification target circles replicated in the same reaction are different, wherein each different amplification target circle produces a different tandem sequence DNA, wherein the presence or absence of different analytes is indicated by the presence orabsence of corresponding tandem sequence DNA. 49. The method of claim 48, wherein replication of each different amplification target circle is primed by a different one of the rolling circle replication primers. 50. The method of claim 1, further comprising, prior to, simultaneous with, or following step (a), bringing into contact one or more first analyte capture agents and one or more first analyte samples, and bringing into contact one or moresecond analyte capture agents and one or more second analyte samples, wherein each analyte capture agent comprises an analyte interaction portion and a capture portion, wherein for each first analyte capture agent there is a matching second analytecapture agent, wherein the analyte interaction portions of the first analyte capture agents interact with the same analyte as the analyte interaction portions of the matching second analyte capture agents, wherein the capture portions of the first andsecond analyte capture agents each interact with a specific binding molecule of one or more of the reporter binding molecules, wherein the capture portions of the first analyte capture agents interact with different specific binding molecules than thecapture portions of the matching second analyte capture agents, wherein each different specific binding molecule is part of a different one of the reporter binding molecules, wherein the amplification target circle of each different reporter bindingmolecule is different, wherein replication of each different amplification target circle is primed by a different one of the rolling circle replication primers, wherein each different amplification target circle produces a different tandem sequence DNA,wherein the amplification target circle of a reporter binding molecule that comprises a specific binding molecule that interacts with an analyte capture agent corresponds to the analyte capture agent, wherein the presence or absence of the same analytein different analyte samples is indicated by the presence or absence of corresponding tandem sequence DNA. 51. The method of claim 50, further comprising mixing one or more of the first analyte samples and one or more of the second analyte samples. 52. The method of claim 50, further comprising mixing the one or more first analyte capture agents and the one or more second analyte capture agents. 53. The method of claim 52, wherein mixing the one or more first analyte capture agents and the one or more second analyte capture agents is accomplished by associating, simultaneously or sequentially, the one or more first analyte captureagents and the one or more second analyte capture agents with the same solid support. 54. The method of claim 50, wherein the tandem sequence DNA corresponding to one of the analytes and produced in association with a first analyte capture agent is in the same location as, and is simultaneously detected with, tandem sequence DNAcorresponding to the same analyte and produced in association with the matching second analyte capture agent, wherein the presence or absence of the same analyte in different analyte samples is indicated by the presence or absence of corresponding tandemsequence DNA. 55. The method of claim 50, wherein the capture portion of each first analyte capture agent is the same, wherein the reporter binding molecules corresponding to the first analyte capture agents are the same, wherein the amplification targetcircles corresponding to the first analyte capture agents are the same, wherein the capture portion of each second analyte capture agent is the same, wherein the reporter binding molecules corresponding to the second analyte capture agents are the same,wherein the amplification target circles corresponding to the second analyte capture agents are the same. 56. The method of claim 1, wherein at least one of the specific binding molecules is an antibody specific for at least one of the analytes. 57. The method of claim 1, wherein at least one of the specific binding molecules is a molecule that specifically binds to at least one of the analytes. 58. The method of claim 1, wherein at least one of the specific binding molecules is a molecule that specifically binds to at least one of the analytes in combination with an accessory molecule. 59. The method of claim 1, wherein the specific binding molecules and analytes interact by binding to each other directly or indirectly. 60. The method of claim 1, wherein at least one accessory molecule is brought into contact with at least one of the analyte samples and at least one of the reporter binding molecules, wherein the accessory molecule affects the interaction of atleast one of the analytes and at least one of the specific binding molecules or at least one of the analyte capture agents. 61. The method of claim 60, wherein the accessory molecule competes with the interaction of at least one of the specific binding molecules or at least one of the analyte capture agents. 62. The method of claim 61, wherein the accessory molecule is an analog of at least one of the analytes. 63. The method of claim 60, wherein the accessory molecule facilitates the interaction of at least one of the specific binding molecules or at least one of the analyte capture agents. 64. The method of claim 60, wherein the accessory molecule is brought into contact with at least one of the analyte samples, at least one of the reporter binding molecules, or both, prior to, simultaneous with, or following step (a). 65. The method of claim 60, wherein the accessory molecule is a protein kinase, a protein phosphatase, an enzyme, or a compound. 66. The method of claim 60, wherein the accessory molecule is at least 20% pure. 67. The method of claim 60, wherein the accessory molecule is at least 50% pure. 68. The method of claim 60, wherein the accessory molecule is at least 80% pure. 69. The method of claim 60, wherein the accessory molecule is at least 90% pure. 70. The method of claim 1, wherein at least one of the analytes is associated with a solid support. 71. The method of claim 70, wherein the solid support comprises one or more reaction chambers, wherein a plurality of the analytes associated with the solid support are associated with the solid support in the same reaction chamber. 72. The method of claim 70, wherein at least one of the analytes associated with the solid support is associated with the solid support indirectly. 73. The method of claim 72, wherein the analytes associated with the solid support interact with analyte capture agents, and wherein the analyte capture agents are associated with the solid support thereby indirectly associating the analyteswith the solid support. 74. The method of claim 1, wherein at least one specific binding molecule interacts with at least one analyte indirectly. 75. The method of claim 74, wherein the analyte interacts with an analyte capture agent, and wherein the specific binding molecule interacts with the analyte capture agent thereby indirectly associating the specific binding molecule with theanalyte. 76. The method of claim 1, wherein at least one of the analytes is a modified form of another analyte, wherein the specific binding molecule of at least one of the reporter binding molecules interacts, directly or indirectly, with the analytethat is a modified form of the other analyte, and wherein the specific binding molecule of another reporter binding molecule interacts, directly or indirectly, with the other analyte. 77. The method of claim 76, wherein the analytes are proteins, wherein the modification of the modified form of the other analyte is a post-translational modification. 78. The method of claim 77, wherein the modification is phosphorylation or glycosylation. 79. The method of claim 1, wherein detection of the tandem sequence DNA is accomplished by mixing a set of detection probes with the tandem sequence DNA under conditions that promote hybridization between the tandem sequence DNA and thedetection probes. 80. The method of claim 79, wherein a plurality of different tandem sequence DNAs are detected separately and simultaneously via multiplex detection. 81. The method of claim 80, wherein the set of detection probes is labeled using combinatorial multicolor coding. 82. The method of claim 1, further comprising, simultaneous with, or following, step (d), bringing into contact a secondary DNA strand displacement primer and the tandem sequence DNA, and incubating under conditions that promote (i)hybridization between the tandem sequence DNA and the secondary DNA strand displacement primer, and (ii) replication of the tandem sequence DNA, wherein replication of the tandem sequence DNA results in the formation of secondary tandem sequence DNA. 83. The method of claim 82, wherein the tandem sequence DNA, secondary tandem sequence DNA, or both, are detected during replication of the amplification target circles. 84. The method of claim 83, wherein the tandem sequence DNA, secondary tandem sequence DNA, or both, are detected by detecting fluorescent moieties incorporated into the tandem sequence DNA, secondary tandem sequence DNA, or both. 85. The method of claim 82, wherein the tandem sequence DNA, secondary tandem sequence DNA, or both, are detected during replication of the tandem sequence DNA. 86. The method of claim 82, wherein at least one of the rolling circle replication primers is a fluorescent quenched primer. 87. The method of claim 82, wherein at least one of the secondary DNA strand displacement primers is a fluorescent quenched primer. 88. The method of claim 82, wherein at least one of the rolling circle replication primers and at least one of the secondary DNA strand displacement primers are fluorescent quenched primers. 89. The method of claim 82, wherein the tandem sequence DNA, secondary tandem sequence DNA, or both, are detected by detecting fluorescent moieties incorporated into the tandem sequence DNA. 90. The method of claim 82, wherein the secondary tandem sequence DNA is replicated to form higher order tandem sequence DNA. 91. The method of claim 90, wherein the amplification target circles, the tandem sequence DNA, and the secondary tandem sequence DNA are replicated simultaneously. 92. The method of claim 90, wherein the tandem sequence DNA, secondary tandem sequence DNA, higher order tandem sequence DNA, or a combination, is detected during replication of the amplification target circles. 93. The method of claim 90, wherein the tandem sequence DNA, secondary tandem sequence DNA, higher order tandem sequence DNA, or a combination, is detected by detecting fluorescent moieties incorporated into the tandem sequence DNA, secondarytandem sequence DNA, higher order tandem sequence DNA, or a combination. 94. The method of claim 90, wherein the tandem sequence DNA, secondary tandem sequence DNA, higher order tandem sequence DNA, or a combination, is detected during replication of the tandem sequence DNA. 95. The method of claim 90, wherein at least one of the rolling circle replication primers is a fluorescent quenched primer. 96. The method of claim 90, wherein at least one of the secondary DNA strand displacement primers is a fluorescent quenched primer. 97. The method of claim 90, wherein at least one of the rolling circle replication primers and at least one of the secondary DNA strand displacement primers are fluorescent quenched primers. 98. The method of claim 90, wherein the tandem sequence DNA, secondary tandem sequence DNA, higher order tandem sequence DNA, or a combination, is detected by detecting fluorescent moieties incorporated into the tandem sequence DNA. 99. The method of claim 1, wherein the tandem sequence DNA is detected during replication of the amplification target circles. 100. The method of claim 99, wherein the tandem sequence DNA is detected by detecting fluorescent moieties incorporated into the tandem sequence DNA. 101. The method of claim 1, wherein at least one of the rolling circle replication primers is a fluorescent quenched primer. 102. The method of claim 1, wherein the tandem sequence DNA is detected by detecting fluorescent moieties incorporated into the tandem sequence DNA. 103. The method of claim 1, wherein the reporter binding molecules are at least 20% pure. 104. The method of claim 1, wherein the reporter binding molecules are at least 50% pure. 105. The method of claim 1, wherein the reporter binding molecules are at least 80% pure. 106. The method of claim 1, wherein the reporter binding molecules are at least 90% pure. 107. A method for detecting one or more analytes, the method comprising (a) bringing into contact one or more analyte samples and one or more analyte capture agents, wherein each analyte capture agent interacts with an analyte directly orindirectly, wherein at least one analyte, if present in the analyte sample, interacts with at least one analyte capture agent, incubating the analyte samples and the analyte capture agents under conditions that promote interaction of the analyte captureagents and analytes, (b) bringing into contact at least one of the analyte samples and one or more reporter binding molecules, wherein each reporter binding molecule comprises a specific binding molecule and an amplification target circle, wherein eachspecific binding molecule interacts with an analyte capture agent directly or indirectly, incubating the analyte samples and the reporter binding molecules under conditions that promote interaction of the specific binding molecules and analyte captureagents, and separating the specific binding molecules that interact with the analyte capture agents from the specific binding molecules that do not interact with the analyte capture agents, (c) decoupling the amplification target circles associated withthe analytes from the specific binding molecules, (d) bringing into contact the decoupled amplification target circles and one or more rolling circle replication primers, wherein the amplification target circles each comprise a single-stranded, circularDNA molecule comprising a primer complement portion, wherein the primer complement portion is complementary to at least one of the rolling circle replication primers, and incubating the rolling circle replication primers and amplification target circlesunder conditions that promote hybridization between the amplification target circles and the rolling circle replication primers, (e) incubating the rolling circle replication primers and amplification target circles under conditions that promotereplication of the amplification target circles, wherein replication of the amplification target circles results in the formation of tandem sequence DNA, wherein detection of tandem sequence DNA indicates the presence of the corresponding analytes. 108. A method for detecting one or more analytes, the method comprising (a) treating one or more analyte samples so that one or more analytes are modified, (b) bringing into contact at least one of the analyte samples and one or more reporterbinding molecules, wherein each reporter binding molecule comprises a specific binding molecule and an amplification target circle, wherein each specific binding molecule interacts with a modified analyte directly or indirectly, incubating the analytesamples and the reporter binding molecules under conditions that promote interaction of the specific binding molecules and modified analytes, and separating the specific binding molecules that interact with the modified analytes from the specific bindingmolecules that do not interact with the modified analytes, (c) decoupling the amplification target circles associated with the analytes from the specific binding molecules, (d) bringing into contact the decoupled amplification target circles and one ormore rolling circle replication primers, wherein the amplification target circles each comprise a single-stranded, circular DNA molecule comprising a primer complement portion, wherein the primer complement portion is complementary to at least one of therolling circle replication primers, and incubating the rolling circle replication primers and amplification target circles under conditions that promote hybridization between the amplification target circles and the rolling circle replication primers,(e) incubating the rolling circle replication primers and amplification target circles under conditions that promote replication of the amplification target circles, wherein replication of the amplification target circles results in the formation oftandem sequence DNA, wherein detection of tandem sequence DNA indicates the presence of the corresponding modified analytes. 109. The method of claim 108, wherein all of the analytes are modified by associating a modifying group to the analytes, wherein the modifying group is the same for all of the analytes, wherein all of the specific binding molecules interactwith the modifying group. 110. A method for detecting one or more analytes, the method comprising (a) bringing into contact one or more analyte samples and a set of analyte capture agents, a set of accessory molecules, or both, wherein each analyte capture agentinteracts with an analyte directly or indirectly, (b) prior to, simultaneous with, or following step (a), bringing into contact at least one of the analyte samples and one or more reporter binding molecules, wherein each reporter binding moleculecomprises a specific binding molecule and an amplification target circle, wherein each specific binding molecule interacts with an analyte directly or indirectly, wherein each accessory molecule affects the interaction of at least one of the analytes andat least one of the specific binding molecules or at least one of the analyte capture agents, (c) simultaneous with, or following, steps (a) and (b), incubating the analyte samples, the analyte capture agents, the accessory molecules, and the reporterbinding molecules under conditions that promote interaction of the specific binding molecules, analytes, analyte capture agents, and accessory molecules, and separating the specific binding molecules that interact with the analytes from the specificbinding molecules that do not interact with the analytes, decoupling the amplification target circles associated with the analytes from the specific binding molecules, (d) bringing into contact the decoupled amplification target circles and one or morerolling circle replication primers, wherein the amplification target circles each comprise a single-stranded, circular DNA molecule comprising a primer complement portion, wherein the primer complement portion is complementary to at least one of therolling circle replication primers, and incubating the rolling circle replication primers and amplification target circles under conditions that promote hybridization between the amplification target circles and the rolling circle replication primers,(e) incubating the reporter binding molecules and amplification target circles under conditions that promote replication of the amplification target circles, wherein replication of the amplification target circles results in the formation of tandemsequence DNA, wherein detection of tandem sequence DNA indicates the presence of the corresponding analytes. 111. The method of claim 110, wherein the analyte capture agents are immobilized on a solid support, wherein the solid support comprises one or more reaction chambers, wherein a plurality of the analyte capture agents are immobilized in thesame reaction chamber of the solid support. 112. The method of claim 111, wherein the analyte capture agents are immobilized to the solid support at a density exceeding 400 different analyte capture agents per cubic centimeter. 113. The method of claim 111, wherein the analyte capture agents are peptides. 114. The method of claim 113, wherein each of the different peptides is at least 4 amino acids in length. 115. The method of claim 114, wherein each different peptide is from about 4 to about 20 amino acids in length. 116. The method of claim 114, wherein each different peptide is at least 10 amino acids in length. 117. The method of claim 114, wherein each different peptide is at least 20 amino acids in length. 118. The method of claim 111, wherein the solid support comprises a plurality of reaction chambers. 119. The method of claim 111, wherein the solid support comprises acrylamide, agarose, cellulose, cellulose, nitrocellulose, glass, gold, polystyrene, polyethylene vinyl acetate, polypropylene, polymethacrylate, polyethylene, polyethyleneoxide, glass, polysilicates, polycarbonates, teflon, fluorocarbons, nylon, silicon rubber, polyanhydrides, polyglycolic acid, polylactic acid, polyorthoesters, functionalized silane, polypropylfumerate, collagen, glycosaminoglycans, or polyamino acids. 120. The method of claim 111, wherein the analyte capture agents in the reaction chambers are at least 20% pure. 121. The method of claim 111, wherein the analyte capture agents in the reaction chambers are at least 50% pure. 122. The method of claim 111, wherein the analyte capture agents in the reaction chambers are at least 80% pure. 123. The method of claim 111, wherein the analyte capture agents in the reaction chambers are at least 90% pure. 124. A method for detecting one or more analytes, the method comprising bringing into contact one or more analyte samples and one or more reporter binding molecules, wherein each reporter binding molecule comprises a specific binding moleculeand an amplification target circle, wherein each specific binding molecule can interact with an analyte directly or indirectly, separating the specific binding molecules that interact with the analytes from the specific binding molecules that do notinteract with the analytes, decoupling the amplification target circles associated with the analytes from the specific binding molecules, replicating the decoupled amplification target circles, wherein replication of the amplification target circlesresults in the formation of tandem sequence DNA, secondary tandem sequence DNA, and higher order tandem sequence DNA, wherein detection of tandem sequence DNA, secondary tandem sequence DNA, and higher order tandem sequence DNA, or a combination,indicates the presence of the corresponding analytes. 125. The method of claim 124, wherein the amplification target circles, the tandem sequence DNA, and the secondary tandem sequence DNA are replicated simultaneously. 126. The method of claim 124, wherein the tandem sequence DNA, secondary tandem sequence DNA, higher order tandem sequence DNA, or a combination, is detected during replication of the amplification target circles. 127. The method of claim 124, wherein the tandem sequence DNA, secondary tandem sequence DNA, higher order tandem sequence DNA, or a combination, is detected by detecting fluorescent moieties incorporated into the tandem sequence DNA, secondarytandem sequence DNA, higher order tandem sequence DNA, or a combination. 128. The method of claim 124, wherein the tandem sequence DNA, secondary tandem sequence DNA, higher order tandem sequence DNA, or a combination, is detected during replication of the tandem sequence DNA. 129. The method of claim 124, wherein at least one of the rolling circle replication primers is a fluorescent quenched primer. 130. The method of claim 124, wherein at least one of the secondary DNA strand displacement primers is a fluorescent quenched primer. 131. The method of claim 124, wherein at least one of the rolling circle replication primers and at least one of the secondary DNA strand displacement primers are fluorescent quenched primers. 132. The method of claim 124, wherein the tandem sequence DNA, secondary tandem sequence DNA, higher order tandem sequence DNA, or a combination, is detected by detecting fluorescent moieties incorporated into the tandem sequence DNA. 133. A method for detecting one or more analytes, the method comprising bringing into contact one or more analyte samples and one or more reporter binding molecules, wherein each reporter binding molecule comprises a specific binding moleculeand an amplification target circle, wherein each specific binding molecule can interact with an analyte directly or indirectly, separating the specific binding molecules that interact with the analytes from the specific binding molecules that do notinteract with the analytes, decoupling the amplification target circles associated with the analytes from the specific binding molecules, replicating the decoupled amplification target circles, wherein replication of the amplification target circlesresults in the formation of tandem sequence DNA, wherein detection of tandem sequence DNA indicates the presence of the corresponding analytes. 134. A method for detecting one or more analytes, the method comprising bringing into contact one or more analyte samples and one or more analyte capture agents, wherein each analyte capture agents can interact with an analyte directly orindirectly, bringing into contact at least one of the analyte samples and one or more reporter binding molecules, wherein each reporter binding molecule comprises a specific binding molecule and an amplification target circle, wherein each specificbinding molecule can interact with an analyte capture agent directly or indirectly, separating the specific binding molecules that interact with the analyte capture agents from the specific binding molecules that do not interact with the analyte captureagents, decoupling the amplification target circles associated with the analytes from the specific binding molecules, replicating the decoupled amplification target circles, wherein replication of the amplification target circles results in the formationof tandem sequence DNA, wherein detection of tandem sequence DNA indicates the presence of the corresponding analytes. 135. A method for detecting one or more analytes, the method comprising treating one or more analyte samples so that one or more analytes are modified, bringing into contact at least one analyte samples and one or more reporter bindingmolecules, wherein each reporter binding molecule comprises a specific binding molecule and an amplification target circle, wherein each specific binding molecule can interact with a modified analyte directly or indirectly, separating the specificbinding molecules that interact with the modified analytes from the specific binding molecules that do not interact with the modified analytes, decoupling the amplification target circles associated with the analytes from the specific binding molecules,replicating the decoupled amplification target circles, wherein replication of the amplification target circles results in the formation of tandem sequence DNA, wherein detection of tandem sequence DNA indicates the presence of the corresponding modifiedanalytes. 136. A method for detecting one or more analytes, the method comprising bringing into contact one or more analyte samples and a set of analyte capture agents, a set of accessory molecules, or both, wherein each analyte capture agent caninteract with an analyte directly or indirectly, bringing into contact at least one of the analyte samples and one or more reporter binding molecules, wherein each reporter binding molecule comprises a specific binding molecule and an amplificationtarget circle, wherein each specific binding molecule can interact with an analyte directly or indirectly, wherein each accessory molecule can affect the interaction of at least one of the analytes and at least one of the specific binding molecules or atleast one of the analyte capture agents, separating the specific binding molecules that interact with the analytes from the specific binding molecules that do not interact with the analytes, decoupling the amplification target circles associated with theanalytes from the specific binding molecules, replicating the decoupled amplification target circles, wherein replication of the amplification target circles results in the formation of tandem sequence DNA, wherein detection of tandem sequence DNAindicates the presence of the corresponding analytes. 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